id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 6972 Graphics crash, macOS 12.4, Intel Iris Plus Graphics chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Aborted Thread 0x0000000110d8a600 (most recent call first): File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/updateloop.py"", line 95 in draw_new_frame Fatal Python error: Segmentation fault {""app_name"":""ChimeraX"",""timestamp"":""2022-05-27 01:14:51.00 -0400"",""app_version"":""1.3.0"",""slice_uuid"":""9596eff5-d2be-396c-9c4e-6177235c3dae"",""build_version"":""1.3.0.0"",""platform"":1,""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":0,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 12.4 (21F79)"",""incident_id"":""C15A2415-1F23-4D5C-B808-E318746681BF"",""name"":""ChimeraX""} { ""uptime"" : 470000, ""procLaunch"" : ""2022-05-26 23:31:56.3744 -0400"", ""procRole"" : ""Foreground"", ""version"" : 2, ""userID"" : 501, ""deployVersion"" : 210, ""modelCode"" : ""MacBookPro16,2"", ""procStartAbsTime"" : 468203221640309, ""coalitionID"" : 1920, ""osVersion"" : { ""train"" : ""macOS 12.4"", ""build"" : ""21F79"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2022-05-27 01:14:24.0111 -0400"", ""incident"" : ""C15A2415-1F23-4D5C-B808-E318746681BF"", ""bug_type"" : ""309"", ""pid"" : 90273, ""procExitAbsTime"" : 474350676690141, ""cpuType"" : ""X86-64"", ""procName"" : ""ChimeraX"", ""procPath"" : ""\/Applications\/ChimeraX-1.3.app\/Contents\/MacOS\/ChimeraX"", ""bundleInfo"" : {""CFBundleShortVersionString"":""1.3.0"",""CFBundleVersion"":""1.3.0.0"",""CFBundleIdentifier"":""edu.ucsf.cgl.ChimeraX""}, ""storeInfo"" : {""deviceIdentifierForVendor"":""8B4529AF-1CFB-5F11-8E79-0A5644571A50"",""thirdParty"":true}, ""parentProc"" : ""launchd"", ""parentPid"" : 1, ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"", ""crashReporterKey"" : ""A43C6006-34B7-90C4-6BD6-971F9B9BE23A"", ""wakeTime"" : 26381, ""bridgeVersion"" : {""build"":""19P5071"",""train"":""6.5""}, ""sleepWakeUUID"" : ""254BDE8C-9D82-4A1A-BF6B-CB4175E21215"", ""sip"" : ""enabled"", ""vmRegionInfo"" : ""0xb8 is not in any region. 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All rights reserved. How to cite UCSF ChimeraX > open > /Users/tatyanabodrug/Downloads/cryosparc_P19_J1031_003_volume_map_sharp.mrc > format mrc Opened cryosparc_P19_J1031_003_volume_map_sharp.mrc as #1, grid size 400,400,400, pixel 1.17, shown at level 0.587, step 2, values float32 > volume flip #1 Opened cryosparc_P19_J1031_003_volume_map_sharp.mrc z flip as #2, grid size 400,400,400, pixel 1.17, shown at step 1, values float32 > ui mousemode right ""map eraser"" > volume erase #2 center 233.13,216.03,244.03 radius 139 outside true Opened cryosparc_P19_J1031_003_volume_map_sharp.mrc z flip copy as #4, grid size 400,400,400, pixel 1.17, shown at step 1, values float32 > volume erase #4 center 237.71,112.06,242.16 radius 42.987 > volume erase #4 center 220.37,112.78,212.69 radius 42.987 > volume erase #4 center 213.35,112.19,226.22 radius 54.732 > volume erase #4 center 133.34,145.63,223.4 radius 54.732 > volume erase #4 center 352.73,214.22,232.39 radius 54.732 > volume erase #4 center 345.23,140.71,199.15 radius 54.732 > volume erase #4 center 352.35,246.24,299.65 radius 54.732 > volume erase #4 center 333.2,133.35,305.16 radius 54.732 > volume erase #4 center 112.23,229.69,299.25 radius 54.732 > volume erase #4 center 120.39,256.71,262.35 radius 54.732 > volume erase #4 center 294.02,285.71,374.51 radius 54.732 > volume erase #4 center 96.424,197.37,165.69 radius 54.732 > volume erase #4 center 303.3,101.49,228.24 radius 54.732 > surface dust #4 size 11.7 > surface dust #4 size 3 > surface dust #4 size 4 > surface dust #4 size 5 > close #1 > close #2 > open /Users/tatyanabodrug/Desktop/model_fitting/pdbs/6tnt.pdb 6tnt.pdb title: Sumoylated apoapc/C with repositioned APC2 WHB domain [more info...] Chain information for 6tnt.pdb #1 --- Chain | Description | UniProt A | anaphase-promoting complex subunit 1 | APC1_HUMAN B | anaphase-promoting complex subunit 11 | APC11_HUMAN C | cell division cycle protein 23 homolog | CDC23_HUMAN D | APC15 | APC15_HUMAN E | anaphase-promoting complex subunit 16 | APC16_HUMAN F | cell division cycle protein 27 homolog | CDC27_HUMAN G | anaphase-promoting complex subunit CDC26 | CDC26_HUMAN H | cell division cycle protein 27 homolog | CDC27_HUMAN I | anaphase-promoting complex subunit 4 | APC4_HUMAN J | cell division cycle protein 16 homolog | CDC16_HUMAN K | cell division cycle protein 16 homolog | CDC16_HUMAN L | anaphase-promoting complex subunit 10 | APC10_HUMAN M | anaphase-promoting complex subunit 13 | APC13_HUMAN N | anaphase-promoting complex subunit 2 | ANC2_HUMAN O | anaphase-promoting complex subunit 5 | APC5_HUMAN P | cell division cycle protein 23 homolog | CDC23_HUMAN T | unidentified peptide | W | anaphase-promoting complex subunit CDC26 | CDC26_HUMAN X | anaphase-promoting complex subunit 7 | APC7_HUMAN Y | anaphase-promoting complex subunit 7 | APC7_HUMAN Non-standard residues in 6tnt.pdb #1 --- ZN — zinc ion > hide atoms > show cartoons > select #1 63822 atoms, 65192 bonds, 41 pseudobonds, 8112 residues, 3 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #1,0.98934,0.069816,-0.12781,13.01,-0.14563,0.4781,-0.86615,275.72,0.00063494,0.87553,0.48317,-59.205 > view matrix models > #1,-0.032966,0.9527,0.30213,-30.982,-0.21706,0.28826,-0.93263,334.19,-0.9756,-0.096326,0.19729,342.89 > view matrix models > #1,-0.23443,0.93103,-0.2797,115.83,-0.40982,-0.35555,-0.84002,465.5,-0.88153,-0.082305,0.4649,274.4 > view matrix models > #1,-0.18775,0.92135,-0.34038,119.95,0.010581,-0.34462,-0.93868,403.97,-0.98216,-0.17984,0.054954,384.6 > view matrix models > #1,-0.3406,0.81359,-0.47123,190.8,-0.059458,-0.51883,-0.85281,431.74,-0.93833,-0.26245,0.22509,360.01 > ui mousemode right ""translate selected models"" > view matrix models > #1,-0.3406,0.81359,-0.47123,190.91,-0.059458,-0.51883,-0.85281,432.46,-0.93833,-0.26245,0.22509,359.84 > view matrix models > #1,-0.3406,0.81359,-0.47123,222.67,-0.059458,-0.51883,-0.85281,489.98,-0.93833,-0.26245,0.22509,410.39 > view matrix models > #1,-0.3406,0.81359,-0.47123,224.35,-0.059458,-0.51883,-0.85281,491.46,-0.93833,-0.26245,0.22509,417.56 > ui mousemode right ""rotate selected models"" > view matrix models > #1,-0.052021,0.95688,-0.28579,112.31,-0.041632,-0.28801,-0.95672,466.71,-0.99778,-0.037872,0.05482,420.23 > view matrix models > #1,0.057421,0.96397,-0.25976,86.139,-0.03022,-0.25839,-0.96557,461.03,-0.99789,0.063294,0.014294,409.94 > view matrix models > #1,-0.10978,0.95098,-0.28912,124.6,-0.07566,-0.29803,-0.95155,473.8,-0.99107,-0.082583,0.10467,417.75 > fitmap #1 inMap #4 Fit molecule 6tnt.pdb (#1) to map cryosparc_P19_J1031_003_volume_map_sharp.mrc z flip copy (#4) using 63822 atoms average map value = 0.7218, steps = 116 shifted from previous position = 7.8 rotated from previous position = 7.71 degrees atoms outside contour = 28283, contour level = 0.58682 Position of 6tnt.pdb (#1) relative to cryosparc_P19_J1031_003_volume_map_sharp.mrc z flip copy (#4) coordinates: Matrix rotation and translation 0.01239040 0.96583206 -0.25887235 100.02477482 -0.12270284 -0.25546698 -0.95899981 478.17787139 -0.99236611 0.04364676 0.11534500 388.31731970 Axis 0.60702707 0.44407529 -0.65902600 Axis point 417.38692737 334.01584219 0.00000000 Rotation angle (degrees) 124.32356702 Shift along axis 17.15351501 > volume #4 color #73fdff > volume #4 color #73fdff32 > volume #4 level 0.9882 > ~select #1 Nothing selected > isolde start > set selectionWidth 4 Removed all altlocs in #1 and reset associated occupancies to 1. ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 546 residues in model #1 to IUPAC-IUB standards. 6tnt.pdb title: Sumoylated apoapc/C with repositioned APC2 WHB domain [more info...] Chain information for 6tnt.pdb --- Chain | Description | UniProt 1.2/A | anaphase-promoting complex subunit 1 | APC1_HUMAN 1.2/B | anaphase-promoting complex subunit 11 | APC11_HUMAN 1.2/C | cell division cycle protein 23 homolog | CDC23_HUMAN 1.2/D | APC15 | APC15_HUMAN 1.2/E | anaphase-promoting complex subunit 16 | APC16_HUMAN 1.2/F | cell division cycle protein 27 homolog | CDC27_HUMAN 1.2/G | anaphase-promoting complex subunit CDC26 | CDC26_HUMAN 1.2/H | cell division cycle protein 27 homolog | CDC27_HUMAN 1.2/I | anaphase-promoting complex subunit 4 | APC4_HUMAN 1.2/J | cell division cycle protein 16 homolog | CDC16_HUMAN 1.2/K | cell division cycle protein 16 homolog | CDC16_HUMAN 1.2/L | anaphase-promoting complex subunit 10 | APC10_HUMAN 1.2/M | anaphase-promoting complex subunit 13 | APC13_HUMAN 1.2/N | anaphase-promoting complex subunit 2 | ANC2_HUMAN 1.2/O | anaphase-promoting complex subunit 5 | APC5_HUMAN 1.2/P | cell division cycle protein 23 homolog | CDC23_HUMAN 1.2/T | unidentified peptide | 1.2/W | anaphase-promoting complex subunit CDC26 | CDC26_HUMAN 1.2/X | anaphase-promoting complex subunit 7 | APC7_HUMAN 1.2/Y | anaphase-promoting complex subunit 7 | APC7_HUMAN Non-standard residues in 6tnt.pdb #1.2 --- ZN — zinc ion Done loading forcefield > addh Summary of feedback from adding hydrogens to 6tnt.pdb #1.2 --- warnings | Not adding hydrogens to /A LYS 71 CB because it is missing heavy- atom bond partners Not adding hydrogens to /A GLU 82 CB because it is missing heavy-atom bond partners Not adding hydrogens to /A ILE 83 CB because it is missing heavy-atom bond partners Not adding hydrogens to /A GLN 109 CB because it is missing heavy-atom bond partners Not adding hydrogens to /A GLN 135 CB because it is missing heavy-atom bond partners 402 messages similar to the above omitted The following atoms were skipped as donors/acceptors due to missing heavy-atom bond partners: /N PRO 16 N; /A PRO 515 N; /N PRO 33 N; /A PRO 993 N; /A PRO 651 N; /D PRO 23 N; /F PRO 700 N; /B PRO 40 N; /L PRO 171 N; /A PRO 206 N notes | No usable SEQRES records for 6tnt.pdb (#1.2) chain A; guessing termini instead No usable SEQRES records for 6tnt.pdb (#1.2) chain B; guessing termini instead No usable SEQRES records for 6tnt.pdb (#1.2) chain C; guessing termini instead No usable SEQRES records for 6tnt.pdb (#1.2) chain D; guessing termini instead No usable SEQRES records for 6tnt.pdb (#1.2) chain E; guessing termini instead 15 messages similar to the above omitted Chain-initial residues that are actual N termini: /A MET 11, /B MET 1, /C PHE 26, /D SER 2, /E ARG 52, /F GLN 5, /G MET 1, /H GLN 5, /I THR 6, /J ASN 2, /K ASN 2, /L THR 3, /M MET 1, /N ARG 15, /O GLY 25, /P PHE 26, /T ALA 1, /W MET 1, /X ASN 36, /Y ASN 36 Chain-initial residues that are not actual N termini: /A LYS 71, /A PRO 206, /A SER 234, /A SER 362, /A ILE 403, /A GLU 422, /A GLN 579, /A ASP 704, /A LEU 747, /A SER 892, /A VAL 923, /A GLU 1011, /A SER 1347, /A LEU 1452, /A SER 1908, /C GLU 509, /F GLN 455, /F THR 691, /H ALA 451, /I ASN 160, /I GLU 473, /J SER 124, /K SER 127, /M GLU 48, /N PRO 50, /N TRP 232, /N ASN 319, /N SER 474, /N SER 499, /N GLU 750, /O PRO 206, /O VAL 458, /P VAL 146, /P THR 511, /X LEU 132, /Y LEU 132 Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /A LEU 1936, /A ALA 34, /A ALA 193, /A LYS 226, /A VAL 281, /A ASN 375, /A THR 416, /A PRO 515, /A THR 678, /A SER 731, /A LEU 887, /A THR 900, /A PRO 993, /A HIS 1333, /A ILE 1439, /A PRO 1902, /B GLU 84, /C ARG 557, /C CYS 500, /D LYS 56, /E PRO 107, /F LEU 755, /F THR 171, /F LEU 682, /G ASP 25, /H ASP 767, /H ASN 175, /I SER 757, /I PRO 146, /I ASN 457, /J TYR 533, /J MET 95, /K ILE 527, /K LEU 93, /L ARG 184, /M GLU 67, /M PRO 39, /N LEU 817, /N PRO 33, /N GLY 191, /N PHE 304, /N THR 443, /N ASP 486, /N ILE 730, /O LEU 755, /O LYS 167, /O GLU 452, /P ALA 538, /P THR 134, /P CYS 500, /T ALA 15, /W LEU 26, /X PRO 540, /X LEU 110, /Y MET 552, /Y LEU 110 6602 hydrogen bonds Adding 'H' to /A LYS 71 Adding 'H' to /A SER 234 Adding 'H' to /A SER 362 Adding 'H' to /A ILE 403 Adding 'H' to /A GLU 422 28 messages similar to the above omitted /A LEU 1936 is not terminus, removing H atom from 'C' /B GLU 84 is not terminus, removing H atom from 'C' /C ARG 557 is not terminus, removing H atom from 'C' /D LYS 56 is not terminus, removing H atom from 'C' /E PRO 107 is not terminus, removing H atom from 'C' 15 messages similar to the above omitted 62845 hydrogens added > set silhouettes false > view > delete ~protein > hide HC > select #1 126755 atoms, 128138 bonds, 36 pseudobonds, 8109 residues, 9 models selected > clipper isolate #1 maskRadius 16 > show ~HC > select /G:1-25 453 atoms, 454 bonds, 25 residues, 1 model selected > select /D:2-56 843 atoms, 854 bonds, 55 residues, 1 model selected > select /E:52-107 888 atoms, 897 bonds, 56 residues, 1 model selected > select /E 888 atoms, 897 bonds, 56 residues, 1 model selected > isolde sim start sel Populating font family aliases took 370 ms. Replace uses of missing font family ""Carlito"" with one that exists to avoid this cost. ISOLDE: started sim > view > view sel > hide ~@CA ISOLDE: paused sim > sequence chain #1.2/E Alignment identifier is 1.2/E > select /E:107 14 atoms, 14 bonds, 1 residue, 1 model selected > select /E:86-107 365 atoms, 370 bonds, 21 pseudobonds, 22 residues, 2 models selected > select /E:72 17 atoms, 17 bonds, 1 residue, 1 model selected > select /E:72-84 203 atoms, 203 bonds, 12 pseudobonds, 13 residues, 2 models selected > select /E:89-90 34 atoms, 33 bonds, 1 pseudobond, 2 residues, 2 models selected > select /E:73-90 285 atoms, 284 bonds, 17 pseudobonds, 18 residues, 2 models selected > select /E:73-90 285 atoms, 284 bonds, 17 pseudobonds, 18 residues, 2 models selected > isolde sim start sel Simulation already running! ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 10 residues in model #1.2 to IUPAC-IUB standards. ISOLDE: stopped sim > select /E:73-90 285 atoms, 284 bonds, 18 residues, 1 model selected > isolde sim start sel ISOLDE: started sim > hide ~@CA ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > select /E:74 17 atoms, 16 bonds, 1 residue, 1 model selected > select /E:52-74 347 atoms, 350 bonds, 23 residues, 1 model selected > select /E:82-83 29 atoms, 28 bonds, 2 residues, 1 model selected > select /E:57-83 439 atoms, 441 bonds, 27 residues, 1 model selected > select /E:57-83 439 atoms, 441 bonds, 27 residues, 1 model selected > isolde sim start sel ISOLDE: started sim > hide ~@CA ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > select /E:76-77 26 atoms, 25 bonds, 2 residues, 1 model selected > select /E:59-77 305 atoms, 307 bonds, 19 residues, 1 model selected > select /E:73 12 atoms, 11 bonds, 1 residue, 1 model selected > select /E:55-73 294 atoms, 296 bonds, 19 residues, 1 model selected > select /E:55-73 294 atoms, 296 bonds, 19 residues, 1 model selected > isolde sim start sel ISOLDE: started sim > hide ~@CA ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB standards. ISOLDE: stopped sim > select /G:1-25 453 atoms, 454 bonds, 25 residues, 1 model selected > view > select /E:52-107 888 atoms, 897 bonds, 56 residues, 1 model selected > select /F:5-755 7083 atoms, 7170 bonds, 2 pseudobonds, 460 residues, 2 models selected > select /Y:36-552 7781 atoms, 7841 bonds, 1 pseudobond, 496 residues, 2 models selected > sequence chain #1.2/Y Alignment identifier is 1.2/Y > select /Y:276-327 809 atoms, 815 bonds, 52 residues, 1 model selected > select /Y:276-552 4333 atoms, 4364 bonds, 277 residues, 1 model selected > select /Y:36-37 32 atoms, 31 bonds, 2 residues, 1 model selected > select /Y:36-274 3441 atoms, 3469 bonds, 1 pseudobond, 218 residues, 2 models selected > select /Y:36-274 3441 atoms, 3469 bonds, 1 pseudobond, 218 residues, 2 models selected > isolde sim start sel ISOLDE: started sim > view sel > hide ~@CA > select /Y:170-174 89 atoms, 88 bonds, 4 pseudobonds, 5 residues, 2 models selected > select /Y:170-226 853 atoms, 856 bonds, 56 pseudobonds, 57 residues, 2 models selected > select /Y:228-236 139 atoms, 141 bonds, 8 pseudobonds, 9 residues, 2 models selected > select /Y:228-245 292 atoms, 298 bonds, 17 pseudobonds, 18 residues, 2 models selected > select /Y:330-335 107 atoms, 107 bonds, 3 pseudobonds, 6 residues, 2 models selected > select /Y:321-335 235 atoms, 235 bonds, 3 pseudobonds, 15 residues, 2 models selected > select /Y:37-44 133 atoms, 133 bonds, 7 pseudobonds, 8 residues, 2 models selected > select /Y:37-54 271 atoms, 272 bonds, 17 pseudobonds, 18 residues, 2 models selected > select /Y:52-60 152 atoms, 151 bonds, 8 pseudobonds, 9 residues, 2 models selected > select /Y:52-67 255 atoms, 254 bonds, 15 pseudobonds, 16 residues, 2 models selected > select /Y:69-70 34 atoms, 33 bonds, 1 pseudobond, 2 residues, 2 models selected > select /Y:69-85 284 atoms, 289 bonds, 16 pseudobonds, 17 residues, 2 models selected > select /Y:86-95 175 atoms, 177 bonds, 9 pseudobonds, 10 residues, 2 models selected > select /Y:86-110 422 atoms, 425 bonds, 24 pseudobonds, 25 residues, 2 models selected > select /Y:134-140 119 atoms, 119 bonds, 6 pseudobonds, 7 residues, 2 models selected > select /Y:134-156 379 atoms, 380 bonds, 22 pseudobonds, 23 residues, 2 models selected > select /Y:157-158 29 atoms, 28 bonds, 1 pseudobond, 2 residues, 2 models selected > select /Y:157-178 355 atoms, 356 bonds, 21 pseudobonds, 22 residues, 2 models selected > select /Y:179-181 65 atoms, 65 bonds, 2 pseudobonds, 3 residues, 2 models selected > select /Y:179-206 452 atoms, 455 bonds, 27 pseudobonds, 28 residues, 2 models selected > select /Y:199-203 73 atoms, 73 bonds, 4 pseudobonds, 5 residues, 2 models selected > select /Y:199-206 114 atoms, 114 bonds, 7 pseudobonds, 8 residues, 2 models selected > view sel > select /Y:194-200 116 atoms, 116 bonds, 6 pseudobonds, 7 residues, 2 models selected > select /Y:194-204 176 atoms, 176 bonds, 10 pseudobonds, 11 residues, 2 models selected > select /Y:207-211 75 atoms, 74 bonds, 4 pseudobonds, 5 residues, 2 models selected > select /Y:207-229 290 atoms, 289 bonds, 22 pseudobonds, 23 residues, 2 models selected > view sel > select /Y:230-238 145 atoms, 147 bonds, 8 pseudobonds, 9 residues, 2 models selected > select /Y:230-256 426 atoms, 433 bonds, 26 pseudobonds, 27 residues, 2 models selected > select /Y:249 7 atoms, 6 bonds, 1 residue, 1 model selected > select /Y:249-256 108 atoms, 107 bonds, 7 pseudobonds, 8 residues, 2 models selected > select /Y:246-248 47 atoms, 47 bonds, 2 pseudobonds, 3 residues, 2 models selected > select /Y:246-250 66 atoms, 66 bonds, 4 pseudobonds, 5 residues, 2 models selected > select /Y:242-246 77 atoms, 78 bonds, 4 pseudobonds, 5 residues, 2 models selected > select /Y:242-247 94 atoms, 96 bonds, 5 pseudobonds, 6 residues, 2 models selected > select /Y:237-239 51 atoms, 52 bonds, 2 pseudobonds, 3 residues, 2 models selected > select /Y:237-243 123 atoms, 125 bonds, 6 pseudobonds, 7 residues, 2 models selected > select /Y:220-224 59 atoms, 58 bonds, 4 pseudobonds, 5 residues, 2 models selected > select /Y:220-226 82 atoms, 81 bonds, 6 pseudobonds, 7 residues, 2 models selected > select /Y:228-232 65 atoms, 65 bonds, 4 pseudobonds, 5 residues, 2 models selected > select /Y:224-232 114 atoms, 114 bonds, 8 pseudobonds, 9 residues, 2 models selected > select /Y:235-239 94 atoms, 97 bonds, 4 pseudobonds, 5 residues, 2 models selected > select /Y:235-244 176 atoms, 180 bonds, 9 pseudobonds, 10 residues, 2 models selected > select /Y:249-252 44 atoms, 43 bonds, 3 pseudobonds, 4 residues, 2 models selected > select /Y:249-256 108 atoms, 107 bonds, 7 pseudobonds, 8 residues, 2 models selected > select /Y:257-260 55 atoms, 54 bonds, 3 pseudobonds, 4 residues, 2 models selected > select /Y:257-276 316 atoms, 315 bonds, 19 pseudobonds, 20 residues, 2 models selected > view sel > select /Y:273-280 116 atoms, 115 bonds, 7 pseudobonds, 8 residues, 2 models selected > select /Y:273-293 328 atoms, 329 bonds, 20 pseudobonds, 21 residues, 2 models selected > view > select /Y:266-271 104 atoms, 103 bonds, 5 pseudobonds, 6 residues, 2 models selected > select /Y:266-276 172 atoms, 171 bonds, 10 pseudobonds, 11 residues, 2 models selected > select /Y:260-265 100 atoms, 99 bonds, 5 pseudobonds, 6 residues, 2 models selected > select /Y:260-269 174 atoms, 173 bonds, 9 pseudobonds, 10 residues, 2 models selected > select /Y:271-275 73 atoms, 72 bonds, 4 pseudobonds, 5 residues, 2 models selected > select /Y:271-287 252 atoms, 253 bonds, 16 pseudobonds, 17 residues, 2 models selected > view sel > select /Y:262-269 144 atoms, 143 bonds, 7 pseudobonds, 8 residues, 2 models selected > select /Y:257-269 218 atoms, 217 bonds, 12 pseudobonds, 13 residues, 2 models selected > select /Y:281-287 108 atoms, 109 bonds, 6 pseudobonds, 7 residues, 2 models selected > select /Y:281-292 190 atoms, 191 bonds, 11 pseudobonds, 12 residues, 2 models selected > select /Y:295-302 121 atoms, 121 bonds, 7 pseudobonds, 8 residues, 2 models selected > select /Y:291-302 198 atoms, 199 bonds, 11 pseudobonds, 12 residues, 2 models selected > view > view orient > select /Y:267-307 654 atoms, 658 bonds, 40 pseudobonds, 41 residues, 2 models selected > select /Y:307-335 429 atoms, 431 bonds, 11 pseudobonds, 29 residues, 2 models selected ISOLDE: paused sim ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 5 residues in model #1.2 to IUPAC-IUB standards. ISOLDE: stopped sim > select /Y 7781 atoms, 7841 bonds, 1 pseudobond, 496 residues, 2 models selected > isolde sim start sel ISOLDE: started sim > hide ~@CA > select /Y:322-323 27 atoms, 26 bonds, 1 pseudobond, 2 residues, 2 models selected > select /Y:322-340 287 atoms, 288 bonds, 18 pseudobonds, 19 residues, 2 models selected > select /Y:311-312 28 atoms, 28 bonds, 1 pseudobond, 2 residues, 2 models selected > select /Y:311-320 142 atoms, 143 bonds, 9 pseudobonds, 10 residues, 2 models selected > select /Y:295-301 107 atoms, 106 bonds, 6 pseudobonds, 7 residues, 2 models selected > select /Y:295-306 202 atoms, 203 bonds, 11 pseudobonds, 12 residues, 2 models selected > select /Y:271-279 125 atoms, 124 bonds, 8 pseudobonds, 9 residues, 2 models selected > select /Y:271-289 288 atoms, 289 bonds, 18 pseudobonds, 19 residues, 2 models selected > select /Y:257-262 89 atoms, 88 bonds, 5 pseudobonds, 6 residues, 2 models selected > select /Y:257-268 206 atoms, 205 bonds, 11 pseudobonds, 12 residues, 2 models selected > select /Y:203-244 601 atoms, 606 bonds, 41 pseudobonds, 42 residues, 2 models selected > select /Y:244-256 185 atoms, 186 bonds, 12 pseudobonds, 13 residues, 2 models selected > view sel > select /Y:236-246 188 atoms, 191 bonds, 10 pseudobonds, 11 residues, 2 models selected > select /Y:236-247 205 atoms, 209 bonds, 11 pseudobonds, 12 residues, 2 models selected > select /Y:229-236 132 atoms, 134 bonds, 7 pseudobonds, 8 residues, 2 models selected > select /Y:229-239 183 atoms, 187 bonds, 10 pseudobonds, 11 residues, 2 models selected ISOLDE: paused sim ISOLDE: resumed sim > select /Y:239-243 96 atoms, 98 bonds, 4 pseudobonds, 5 residues, 2 models selected > select /Y:237-243 123 atoms, 125 bonds, 6 pseudobonds, 7 residues, 2 models selected > select /Y:239-247 159 atoms, 163 bonds, 8 pseudobonds, 9 residues, 2 models selected > select /Y:238-247 175 atoms, 179 bonds, 9 pseudobonds, 10 residues, 2 models selected ISOLDE: paused sim ISOLDE: resumed sim > view sel > view > select /Y:250-254 71 atoms, 70 bonds, 4 pseudobonds, 5 residues, 2 models selected > select /Y:250-256 101 atoms, 100 bonds, 6 pseudobonds, 7 residues, 2 models selected > view sel > select /Y:215-257 609 atoms, 616 bonds, 42 pseudobonds, 43 residues, 2 models selected > select /Y:257-272 260 atoms, 259 bonds, 15 pseudobonds, 16 residues, 2 models selected > select /Y:266-275 161 atoms, 160 bonds, 9 pseudobonds, 10 residues, 2 models selected > select /Y:266-278 201 atoms, 200 bonds, 12 pseudobonds, 13 residues, 2 models selected > view sel > select /Y:275-289 222 atoms, 223 bonds, 14 pseudobonds, 15 residues, 2 models selected > select /Y:275-293 290 atoms, 291 bonds, 18 pseudobonds, 19 residues, 2 models selected > view sel > select /Y:282 20 atoms, 20 bonds, 1 residue, 1 model selected > select /Y:275-282 119 atoms, 120 bonds, 7 pseudobonds, 8 residues, 2 models selected > select /Y:282-291 150 atoms, 150 bonds, 9 pseudobonds, 10 residues, 2 models selected > select /Y:282-293 191 atoms, 191 bonds, 11 pseudobonds, 12 residues, 2 models selected > view sel > select /Y:275-280 78 atoms, 77 bonds, 5 pseudobonds, 6 residues, 2 models selected > select /Y:275-283 143 atoms, 144 bonds, 8 pseudobonds, 9 residues, 2 models selected > select /Y:288-292 82 atoms, 81 bonds, 4 pseudobonds, 5 residues, 2 models selected > select /Y:288-302 245 atoms, 246 bonds, 14 pseudobonds, 15 residues, 2 models selected > select /Y:307-316 149 atoms, 150 bonds, 9 pseudobonds, 10 residues, 2 models selected > select /Y:307-326 285 atoms, 286 bonds, 19 pseudobonds, 20 residues, 2 models selected > view sel > select /Y:251-297 739 atoms, 741 bonds, 46 pseudobonds, 47 residues, 2 models selected > select /Y:297-306 170 atoms, 171 bonds, 9 pseudobonds, 10 residues, 2 models selected > select /Y:278-280 41 atoms, 40 bonds, 2 pseudobonds, 3 residues, 2 models selected > select /Y:278-285 123 atoms, 124 bonds, 7 pseudobonds, 8 residues, 2 models selected > select /Y:287 14 atoms, 13 bonds, 1 residue, 1 model selected > select /Y:287-297 180 atoms, 180 bonds, 10 pseudobonds, 11 residues, 2 models selected > select /Y:301-304 66 atoms, 67 bonds, 3 pseudobonds, 4 residues, 2 models selected > select /Y:301-306 107 atoms, 108 bonds, 5 pseudobonds, 6 residues, 2 models selected > select /Y:307 7 atoms, 6 bonds, 1 residue, 1 model selected > select /Y:307-316 149 atoms, 150 bonds, 9 pseudobonds, 10 residues, 2 models selected > select /Y:318-320 38 atoms, 37 bonds, 2 pseudobonds, 3 residues, 2 models selected > select /Y:318-332 229 atoms, 229 bonds, 14 pseudobonds, 15 residues, 2 models selected > select /Y:334-337 59 atoms, 58 bonds, 3 pseudobonds, 4 residues, 2 models selected > select /Y:334-343 155 atoms, 158 bonds, 9 pseudobonds, 10 residues, 2 models selected > select /Y:331-338 129 atoms, 130 bonds, 7 pseudobonds, 8 residues, 2 models selected > select /Y:331-341 168 atoms, 170 bonds, 10 pseudobonds, 11 residues, 2 models selected > select /Y:344-350 93 atoms, 94 bonds, 6 pseudobonds, 7 residues, 2 models selected > select /Y:344-356 203 atoms, 206 bonds, 12 pseudobonds, 13 residues, 2 models selected > select /Y:357-363 110 atoms, 110 bonds, 6 pseudobonds, 7 residues, 2 models selected > select /Y:357-369 211 atoms, 211 bonds, 12 pseudobonds, 13 residues, 2 models selected > select /Y:371-375 68 atoms, 67 bonds, 4 pseudobonds, 5 residues, 2 models selected > select /Y:371-389 295 atoms, 294 bonds, 18 pseudobonds, 19 residues, 2 models selected > select /Y:356-392 570 atoms, 570 bonds, 36 pseudobonds, 37 residues, 2 models selected > select /Y:392-406 255 atoms, 257 bonds, 14 pseudobonds, 15 residues, 2 models selected > view sel > select /Y:407-411 78 atoms, 78 bonds, 4 pseudobonds, 5 residues, 2 models selected > select /Y:407-428 336 atoms, 337 bonds, 21 pseudobonds, 22 residues, 2 models selected > view sel > select /Y:399-401 53 atoms, 52 bonds, 2 pseudobonds, 3 residues, 2 models selected > select /Y:399-406 131 atoms, 131 bonds, 7 pseudobonds, 8 residues, 2 models selected > select /Y:407-411 78 atoms, 78 bonds, 4 pseudobonds, 5 residues, 2 models selected > select /Y:400-411 199 atoms, 200 bonds, 11 pseudobonds, 12 residues, 2 models selected > select /Y:410-419 157 atoms, 158 bonds, 9 pseudobonds, 10 residues, 2 models selected > select /Y:407-419 199 atoms, 200 bonds, 12 pseudobonds, 13 residues, 2 models selected > select /Y:418-432 221 atoms, 220 bonds, 14 pseudobonds, 15 residues, 2 models selected > select /Y:418-437 313 atoms, 313 bonds, 19 pseudobonds, 20 residues, 2 models selected > select /Y:438-447 136 atoms, 135 bonds, 9 pseudobonds, 10 residues, 2 models selected > select /Y:438-452 206 atoms, 205 bonds, 14 pseudobonds, 15 residues, 2 models selected > select /Y:441-442 27 atoms, 26 bonds, 1 pseudobond, 2 residues, 2 models selected > select /Y:438-442 51 atoms, 50 bonds, 4 pseudobonds, 5 residues, 2 models selected > select /Y:384-392 144 atoms, 143 bonds, 8 pseudobonds, 9 residues, 2 models selected > select /Y:384-393 163 atoms, 162 bonds, 9 pseudobonds, 10 residues, 2 models selected > select /Y:398-406 146 atoms, 146 bonds, 8 pseudobonds, 9 residues, 2 models selected > select /Y:398-406 146 atoms, 146 bonds, 8 pseudobonds, 9 residues, 2 models selected ISOLDE: paused sim ISOLDE: resumed sim > select /Y:407-412 85 atoms, 85 bonds, 5 pseudobonds, 6 residues, 2 models selected > select /Y:407-422 235 atoms, 236 bonds, 15 pseudobonds, 16 residues, 2 models selected > select /Y:426-432 98 atoms, 97 bonds, 6 pseudobonds, 7 residues, 2 models selected > select /Y:426-439 207 atoms, 207 bonds, 13 pseudobonds, 14 residues, 2 models selected > select /Y:441-444 60 atoms, 59 bonds, 3 pseudobonds, 4 residues, 2 models selected > select /Y:441-452 182 atoms, 181 bonds, 11 pseudobonds, 12 residues, 2 models selected > select /Y:457-463 114 atoms, 113 bonds, 6 pseudobonds, 7 residues, 2 models selected > select /Y:457-471 246 atoms, 245 bonds, 14 pseudobonds, 15 residues, 2 models selected > select /Y:468-476 133 atoms, 134 bonds, 8 pseudobonds, 9 residues, 2 models selected > select /Y:468-485 285 atoms, 286 bonds, 17 pseudobonds, 18 residues, 2 models selected > select /Y:479-484 101 atoms, 100 bonds, 5 pseudobonds, 6 residues, 2 models selected > select /Y:479-485 120 atoms, 119 bonds, 6 pseudobonds, 7 residues, 2 models selected > view sel > select /Y:433-490 912 atoms, 915 bonds, 57 pseudobonds, 58 residues, 2 models selected > select /Y:433-495 989 atoms, 993 bonds, 62 pseudobonds, 63 residues, 2 models selected > select /Y:483 10 atoms, 9 bonds, 1 residue, 1 model selected > select /Y:483-496 226 atoms, 226 bonds, 13 pseudobonds, 14 residues, 2 models selected > view sel > select /Y:499-506 127 atoms, 126 bonds, 7 pseudobonds, 8 residues, 2 models selected > select /Y:490-506 269 atoms, 269 bonds, 16 pseudobonds, 17 residues, 2 models selected > select /Y:507-513 110 atoms, 110 bonds, 6 pseudobonds, 7 residues, 2 models selected > select /Y:507-519 206 atoms, 207 bonds, 12 pseudobonds, 13 residues, 2 models selected > select /Y:517-523 107 atoms, 107 bonds, 6 pseudobonds, 7 residues, 2 models selected > select /Y:517-535 292 atoms, 294 bonds, 18 pseudobonds, 19 residues, 2 models selected > select /Y:524-527 68 atoms, 68 bonds, 3 pseudobonds, 4 residues, 2 models selected > select /Y:524-535 185 atoms, 186 bonds, 11 pseudobonds, 12 residues, 2 models selected > select /Y:537-545 132 atoms, 132 bonds, 8 pseudobonds, 9 residues, 2 models selected > select /Y:537-552 246 atoms, 246 bonds, 15 pseudobonds, 16 residues, 2 models selected ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.3 (2021-12-08) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 INTEL-18.7.4 OpenGL renderer: Intel(R) Iris(TM) Plus Graphics OpenGL Engine OpenGL vendor: Intel Inc.Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro16,2 Processor Name: Quad-Core Intel Core i5 Processor Speed: 2 GHz Number of Processors: 1 Total Number of Cores: 4 L2 Cache (per Core): 512 KB L3 Cache: 6 MB Hyper-Threading Technology: Enabled Memory: 16 GB System Firmware Version: 1731.120.10.0.0 (iBridge: 19.16.15071.0.0,0) OS Loader Version: 540.120.3~6 Software: System Software Overview: System Version: macOS 12.4 (21F79) Kernel Version: Darwin 21.5.0 Time since boot: 9 days 9:50 Graphics/Displays: Intel Iris Plus Graphics: Chipset Model: Intel Iris Plus Graphics Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x8a53 Revision ID: 0x0007 Metal Family: Supported, Metal GPUFamily macOS 2 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Framebuffer Depth: 30-Bit Color (ARGB2101010) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal HP 27er: Resolution: 1600 x 900 UI Looks like: 1600 x 900 @ 60.00Hz Framebuffer Depth: 30-Bit Color (ARGB2101010) Display Serial Number: 3CM6160MVY Mirror: Off Online: Yes Rotation: Supported Adapter Type: DVI or HDMI Adapter Firmware Version: ff.c1 Locale: (None, 'UTF-8') PyQt5 5.15.2, Qt 5.15.2 Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.2 Babel: 2.9.1 backcall: 0.2.0 blockdiag: 2.0.1 certifi: 2021.5.30 cftime: 1.5.1.1 charset-normalizer: 2.0.9 ChimeraX-AddCharge: 1.2.2 ChimeraX-AddH: 2.1.11 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.2.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.31 ChimeraX-AtomicLibrary: 4.2 ChimeraX-AtomSearch: 2.0 ChimeraX-AtomSearchLibrary: 1.0 ChimeraX-AxesPlanes: 2.0 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.0 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.6.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.1 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.2 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.2.2 ChimeraX-Clipper: 0.17.0 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5 ChimeraX-CommandLine: 1.1.5 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.3 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0 ChimeraX-DataFormats: 1.2.2 ChimeraX-Dicom: 1.0 ChimeraX-DistMonitor: 1.1.5 ChimeraX-DistUI: 1.0 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0 ChimeraX-FunctionKey: 1.0 ChimeraX-Geometry: 1.1 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1 ChimeraX-Hbonds: 2.1.2 ChimeraX-Help: 1.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ISOLDE: 1.3 ChimeraX-ItemsInspection: 1.0 ChimeraX-Label: 1.1 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.4 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.1 ChimeraX-Map: 1.1 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1 ChimeraX-Markers: 1.0 ChimeraX-Mask: 1.0 ChimeraX-MatchMaker: 2.0.4 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.4 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.2.6 ChimeraX-ModelPanel: 1.2.1 ChimeraX-ModelSeries: 1.0 ChimeraX-Mol2: 2.0 ChimeraX-Morph: 1.0 ChimeraX-MouseModes: 1.1 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0.2 ChimeraX-OpenCommand: 1.7 ChimeraX-PDB: 2.6.5 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.0.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0.1 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.4.6 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0 ChimeraX-Shortcuts: 1.1 ChimeraX-ShowAttr: 1.0 ChimeraX-ShowSequences: 1.0 ChimeraX-SideView: 1.0 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.6.1 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-Struts: 1.0 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1 ChimeraX-ToolshedUtils: 1.2 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.13.7 ChimeraX-uniprot: 2.2 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 1.0.1 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0 ChimeraX-WebServices: 1.0 ChimeraX-Zone: 1.0 colorama: 0.4.4 cxservices: 1.1 cycler: 0.11.0 Cython: 0.29.24 decorator: 5.1.0 docutils: 0.17.1 filelock: 3.0.12 funcparserlib: 0.3.6 grako: 3.16.5 h5py: 3.6.0 html2text: 2020.1.16 idna: 3.3 ihm: 0.21 imagecodecs: 2021.4.28 imagesize: 1.3.0 ipykernel: 5.5.5 ipython: 7.23.1 ipython-genutils: 0.2.0 jedi: 0.18.0 Jinja2: 3.0.1 jupyter-client: 6.1.12 jupyter-core: 4.9.1 kiwisolver: 1.3.2 lxml: 4.6.3 lz4: 3.1.3 MarkupSafe: 2.0.1 matplotlib: 3.4.3 matplotlib-inline: 0.1.3 msgpack: 1.0.2 netCDF4: 1.5.7 networkx: 2.6.3 numexpr: 2.8.0 numpy: 1.21.2 openvr: 1.16.801 packaging: 21.0 ParmEd: 3.2.0 parso: 0.8.3 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 8.3.2 pip: 21.2.4 pkginfo: 1.7.1 prompt-toolkit: 3.0.23 psutil: 5.8.0 ptyprocess: 0.7.0 pycollada: 0.7.1 pydicom: 2.1.2 Pygments: 2.10.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.6 PyQt5-commercial: 5.15.2 PyQt5-sip: 12.8.1 PyQtWebEngine-commercial: 5.15.2 python-dateutil: 2.8.2 pytz: 2021.3 pyzmq: 22.3.0 qtconsole: 5.1.1 QtPy: 1.11.3 RandomWords: 0.3.0 requests: 2.26.0 scipy: 1.7.1 setuptools: 57.5.0 sfftk-rw: 0.7.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 4.2.0 sphinx-autodoc-typehints: 1.12.0 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 2.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 suds-jurko: 0.6 tifffile: 2021.4.8 tinyarray: 1.2.3 tornado: 6.1 traitlets: 5.1.1 urllib3: 1.26.7 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.37.0 wheel-filename: 1.3.0 }}} " defect closed normal Graphics nonchimerax all ChimeraX